User: likoo27

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likoo270
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Posts by likoo27

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Comment: C: GeneMark-ES command line errors while executing program
... downloaded it from their site, copied gm_key to Home and installed all modules that are written in README. Operating system is Ubuntu 18.10 ...
written 4 weeks ago by likoo270
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GeneMark-ES command line errors while executing program
... Hello, I tried to use Gene-Mark-ES but for some reason errors keep showing up and since I have zero knowleadge of Perl I'm lost what to do. We tried the following commands with such results: 1. **~/Programs/genemark-es/linux_32$ ./gmes_petap.pl --ES --fungus --sequence Canu_Pilon.fna (same for li ...
annotation fungus genemark-es genemark written 4 weeks ago by likoo270
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Comment: C: Second assembly from existing contigs
... Thank you, I will check out those tools ...
written 3 months ago by likoo270
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Comment: C: Second assembly from existing contigs
... I so sorry for not providing more information. Haploid geenome calculated with k=20 is 13,444,390 bp. As for the coverage I'm actually not sure how to check it especially after using canu and pilon. Should I map the reads back to the assembly? I just recently started with boinformatics so I still do ...
written 3 months ago by likoo270
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Second assembly from existing contigs
... My promotor told to try and do the assembly from the first round of assemblies. What i have are contigs : 1. created using Nanopore reads and assemblied in Canu 2. contigs from Canu corrected with PE reads using Pilon 3. contigs from SPAdes assembly using PE reads 4. contigs from hybrid SPAdes usin ...
genome assembly written 3 months ago by likoo270 • updated 3 months ago by colindaven1.0k
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Alignment to contings with Illumina pe with bwa or minimap2?
... Hello :) I'm pretty new to the stuff and after reading some papers and posts I'm still not sure what I should do so maybe somebody with more experience could shed some light. After I got my contings with Canu I would liike to use Pilon and polish them with Illumina reads. After trimming and qualit ...
minimap2 pilon alignment bwa canu written 4 months ago by likoo270 • updated 4 months ago by h.mon23k

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